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- PDB-8urv: Solution NMR structure of pro-IL-18 -

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Basic information

Entry
Database: PDB / ID: 8urv
TitleSolution NMR structure of pro-IL-18
ComponentsInterleukin-18
KeywordsIMMUNE SYSTEM / Interleukin-18 / beta-trefoil
Function / homology
Function and homology information


interleukin-18 receptor binding / Interleukin-18 signaling / positive regulation of tissue remodeling / positive regulation of T-helper 1 cell cytokine production / positive regulation of T-helper 2 cell differentiation / positive regulation of macrophage derived foam cell differentiation / positive regulation of interleukin-13 production / interleukin-18-mediated signaling pathway / positive regulation of neuroinflammatory response / neutrophil activation ...interleukin-18 receptor binding / Interleukin-18 signaling / positive regulation of tissue remodeling / positive regulation of T-helper 1 cell cytokine production / positive regulation of T-helper 2 cell differentiation / positive regulation of macrophage derived foam cell differentiation / positive regulation of interleukin-13 production / interleukin-18-mediated signaling pathway / positive regulation of neuroinflammatory response / neutrophil activation / negative regulation of myoblast differentiation / Interleukin-1 processing / positive regulation of NK T cell proliferation / sleep / triglyceride homeostasis / positive regulation of natural killer cell proliferation / natural killer cell activation / positive regulation of granulocyte macrophage colony-stimulating factor production / type 2 immune response / positive regulation of tyrosine phosphorylation of STAT protein / T-helper 1 type immune response / natural killer cell mediated cytotoxicity / positive regulation of activated T cell proliferation / Interleukin-10 signaling / positive regulation of interleukin-17 production / Pyroptosis / establishment of skin barrier / regulation of cell adhesion / Purinergic signaling in leishmaniasis infection / positive regulation of chemokine production / cholesterol homeostasis / cytokine activity / positive regulation of smooth muscle cell proliferation / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of type II interferon production / positive regulation of inflammatory response / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / positive regulation of cold-induced thermogenesis / angiogenesis / Interleukin-4 and Interleukin-13 signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell population proliferation / defense response to Gram-positive bacterium / inflammatory response / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / cytosol
Similarity search - Function
Interleukin-18 / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBonin, J.P. / Aramini, J.M. / Kay, L.E.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Immunity / Year: 2024
Title: Structural transitions enable interleukin-18 maturation and signaling.
Authors: Ying Dong / Jeffrey P Bonin / Pascal Devant / Zhuoyi Liang / Alexander I M Sever / Julian Mintseris / James M Aramini / Gang Du / Stephen P Gygi / Jonathan C Kagan / Lewis E Kay / Hao Wu /
Abstract: Several interleukin-1 (IL-1) family members, including IL-1β and IL-18, require processing by inflammasome-associated caspases to unleash their activities. Here, we unveil, by cryoelectron ...Several interleukin-1 (IL-1) family members, including IL-1β and IL-18, require processing by inflammasome-associated caspases to unleash their activities. Here, we unveil, by cryoelectron microscopy (cryo-EM), two major conformations of the complex between caspase-1 and pro-IL-18. One conformation is similar to the complex of caspase-4 and pro-IL-18, with interactions at both the active site and an exosite (closed conformation), and the other only contains interactions at the active site (open conformation). Thus, pro-IL-18 recruitment and processing by caspase-1 is less dependent on the exosite than the active site, unlike caspase-4. Structure determination by nuclear magnetic resonance uncovers a compact fold of apo pro-IL-18, which is similar to caspase-1-bound pro-IL-18 but distinct from cleaved IL-18. Binding sites for IL-18 receptor and IL-18 binding protein are only formed upon conformational changes after pro-IL-18 cleavage. These studies show how pro-IL-18 is selected as a caspase-1 substrate, and why cleavage is necessary for its inflammatory activity.
History
DepositionOct 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interleukin-18


Theoretical massNumber of molelcules
Total (without water)22,3501
Polymers22,3501
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Interleukin-18


Mass: 22350.225 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL18 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14116

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
212isotropic33D HCH NOESY
121isotropic33D HNH NOESY
131isotropic33D NNH NOESY
141isotropic12D NH HSQC
252isotropic32D CH HSQC
161isotropic13D HNCO
171isotropic13D HN(CA)CO
181isotropic13D CBCA(CO)NH
191isotropic13D HN(CA)CB
1101isotropic13D HNN
1121isotropic13D HBHA(CO)NH
1111isotropic23D C(CO)NH TOCSY
1131isotropic23D H(CCO)NH TOCSY
1141isotropic23D C(CA)NH TOCSY
2152isotropic32D CB(CGCD)HD
2162isotropic32D CB(CGCDCE)HE
2172isotropic12D CBCG(CE)HE
1183isotropic32D CH CT-HSQC

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-13C; U-15N] pro-interleukin-18, 20 mM MES, 50 mM potassium chloride, 10 mM DTT, 97% H2O/3% D2O15N, 13C in H2O97% H2O/3% D2O
solution20.5 mM [U-13C; U-15N] pro-interleukin-18, 20 mM MES, 50 mM potassium chloride, 10 mM DTT, 100% D2O15N, 13C in D2O100% D2O
solution30.5 mM [5% U-13C; U-15N] pro-interleukin-18, 20 mM MES, 50 mM potassium chloride, 10 mM DTT, 97% H2O/3% D2O15N, 5% 13C in H2O97% H2O/3% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMpro-interleukin-18[U-13C; U-15N]1
20 mMMESnatural abundance1
50 mMpotassium chloridenatural abundance1
10 mMDTTnatural abundance1
0.5 mMpro-interleukin-18[U-13C; U-15N]2
20 mMMESnatural abundance2
50 mMpotassium chloridenatural abundance2
10 mMDTTnatural abundance2
0.5 mMpro-interleukin-18[5% U-13C; U-15N]3
20 mMMESnatural abundance3
50 mMpotassium chloridenatural abundance3
10 mMDTTnatural abundance3
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
150 mMH2O6.51 atm298.1 K
250 mMD2O6.1 pD1 atm298.1 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE III HDBrukerAVANCE III HD80015 mM TCI-XYZ
Bruker AVANCE III HDBrukerAVANCE III HD60025 mM TCI-XYZ
Bruker AVANCE NEOBrukerAVANCE NEO100035 mM TCI-XYZ

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Processing

NMR software
NameVersionDeveloperClassification
I-PINELee, Bahrami, Dashti, Eghbalnia, Tonelli, Westler and Markleychemical shift assignment
CYANA3.98.15Herrmann, Guntert and Wuthrichstructure calculation
Rosetta3Leaver-Fay et al.refinement
NMRFAM-SPARKYLee, Tonelli and Markleypeak picking
RefinementMethod: simulated annealing / Software ordinal: 3 / Details: FastRelax with constraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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